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BrooksLabUCSC
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flair
Full-Length Alternative Isoform analysis of RNA
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Refactor branch with fixes for #290 and #291
#292
Jeltje
closed
10 months ago
0
ssUtils.py gtfToSSBed crashes if gtf doesn't have transcript_id
#291
diekhans
closed
10 months ago
1
flair correct crash with AttributeError: 'bool' object has no attribute 'find_overlap'
#290
diekhans
closed
10 months ago
1
Refactor - improved error messaging
#289
Jeltje
closed
10 months ago
0
The results of my test_output are not consisitent with the oferred test_expected. Why?
#288
qingwangchen
closed
6 months ago
1
Refactor
#287
Jeltje
closed
10 months ago
0
Refactor
#286
Jeltje
closed
10 months ago
0
diff_iso_usage documentation does not clear describe what it does
#285
diekhans
opened
10 months ago
0
merging of transcript ids and gene ids is frustrating to use
#284
diekhans
closed
7 months ago
2
diff_iso_usage does not include header in output files
#283
diekhans
opened
10 months ago
0
diffsplice_fishers_exact generates bogus error if input file is missing
#282
diekhans
opened
10 months ago
1
`'run_id' is not defined` error while running `collapse-range`
#281
lvclark
closed
10 months ago
2
flair collapse creates invalid isoforms names that cause GTF conversion to fail
#280
diekhans
closed
9 months ago
0
can't keep intermediate files when calling correct from flair
#279
diekhans
opened
10 months ago
1
accept BED9 as well as BED6 for splice junctions
#278
diekhans
opened
10 months ago
0
FLAIR need obvious succes or failure message
#277
diekhans
closed
10 months ago
2
FLAIR logging is very hard to use
#276
diekhans
opened
10 months ago
0
FLAIR silently continues if no short read junctions are added
#275
diekhans
opened
10 months ago
0
flair correct claims success even when there is an error
#274
diekhans
opened
10 months ago
0
Please do not guess file types
#273
diekhans
opened
10 months ago
1
junctions_from_sam creates invalid BEDs that are silently ignored
#272
diekhans
closed
10 months ago
5
flair 123 appears not to use splice junctions
#271
diekhans
closed
11 months ago
1
flair correct documention doesn't define what <prefix>_ is
#270
diekhans
opened
11 months ago
0
flair 123 is horribly hard to use
#269
diekhans
opened
11 months ago
1
alarming "errors" when running multiple modules
#268
diekhans
opened
11 months ago
0
Error while running collapse
#267
kundariyahardik
closed
9 months ago
3
diffsplice output format not documented
#266
diekhans
opened
11 months ago
0
Questions about flair collapse in regards of TSS/TES calling algorithm
#265
seungbeom-han
opened
11 months ago
3
Identification of full-length intergenic isoform
#264
Dongxu-Zheng
closed
5 months ago
1
TypeError: get_sequence_with_variants() takes 2 positional arguments but 3 were given
#263
youyupei
closed
10 months ago
2
Flair collapse returns isoform as same as reference
#262
NHoang98
closed
9 months ago
2
Error in filter_isoforms_by_proportion_of_gene_expr.py
#261
eschiks
closed
1 year ago
1
Feature request: define group for diffExp contrast
#260
skchronicles
closed
1 year ago
5
/Error at the FLAIR collapse step (no data in output files)
#259
pothepanda09
closed
1 year ago
2
Fresh flair install fails align test. [makefile:26: test-align] Error 1
#258
Hans4984
closed
9 months ago
3
Collapse creating combined isoforms
#257
eschiks
closed
1 year ago
1
Question regarding number of reads.
#256
eprdz
opened
1 year ago
0
Issues when running diff_iso_usage, needs to run identify_annotated_gene.py first?
#255
CWYuan08
closed
1 year ago
1
Splicing events belong to more than 1 gene
#254
orbitalse
opened
1 year ago
0
diffSplice: start coordinates > end coordinates
#253
orbitalse
opened
1 year ago
0
FileNotFoundError: [Errno 2] No such file or directory: 'linker'
#252
saizalbert
closed
1 year ago
1
Update count_sam_transcripts.py
#251
listen2099
closed
9 months ago
1
diffsplice_fishers_exact error when dealing with ir.events.quant.tsv
#250
QingCheZhang
opened
1 year ago
2
Unable to install Flair using bioconda
#249
jwyli
closed
1 year ago
1
predictproductivity python script error after flair collapse step
#248
BijalThakkar
closed
1 year ago
0
Revert "Stranded alignment for dRNA in flair quantify"
#247
MViscardi-UCSC
closed
1 year ago
0
Stranded alignment for dRNA in flair quantify
#246
MViscardi-UCSC
closed
1 year ago
1
Unable to find minimap2 in conda environment
#245
RDorney
closed
1 year ago
0
"Superset isoform" definition in flair filter_collapsed_isoforms.py
#244
mariachiaragrieco
opened
1 year ago
2
Testing Flair: missing file
#243
RDorney
closed
1 year ago
2
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